libSBML Python API  5.10.0
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libsbml.SBMLDocument Class Reference
Inheritance diagram for libsbml.SBMLDocument:
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Detailed Description

{core}

Container for an SBML document and interface for global operations on SBML documents.

LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). The two primary means of reading an SBML model, SBMLReader.readSBML() and SBMLReader.readSBMLFromString(), both return a pointer to an SBMLDocument object. From there, callers can inquire about any errors encountered (e.g., using SBMLDocument.getNumErrors()), access the Model object, and perform other actions such as consistency-checking and model translation.

When creating fresh models programmatically, the starting point is typically the creation of an SBMLDocument object instance. The SBMLDocument constructor accepts arguments for the SBML Level and Version of the model to be created. After creating the SBMLDocument object, calling programs then typically call SBMLDocument.createModel() almost immediately, and then proceed to call the methods on the Model object to fill out the model's contents.

SBMLDocument corresponds roughly to the class Sbml defined in the SBML Level 2 specification and SBML in the Level 3 specification. It does not have a direct correspondence in SBML Level 1. (However, to make matters simpler for applications, libSBML creates an SBMLDocument no matter whether the model is Level 1, Level 2 or Level 3.) In its barest form, when written out in XML format for (e.g.) SBML Level 2 Version 4, the corresponding structure is the following:

<sbml xmlns='http://www.sbml.org/sbml/level2/version4' level='2' version='4'>
  ...
</sbml>

SBMLDocument is derived from SBase, and therefore contains the usual SBase attributes (in SBML Level 2 and Level 3) of 'metaid' and 'sboTerm', as well as the subelements 'notes' and 'annotation'. It also contains the attributes 'level' and 'version' indicating the Level and Version of the SBML data structure. These can be accessed using the methods defined by the SBase class for that purpose.

Consistency and adherence to SBML specifications

One of the most important features of libSBML is its ability to perform SBML validation to ensure that a model adheres to the SBML specification for whatever Level+Version combination the model uses. SBMLDocument provides the methods for running consistency-checking and validation rules on the SBML content.

First, a brief explanation of the rationale is in order. In libSBML versions up to and including the version 3.3.x series, the individual methods for creating and setting attributes and other components were quite lenient, and allowed a caller to compose SBML entities that might not, in the end, represent valid SBML. This allowed applications the freedom to do things such as save incomplete models (which is useful when models are being developed over long periods of time). In the version 4.x series, libSBML is somewhat stricter, but still permits structures to be created independently and the results to be combined in a separate step. In all these cases, it means that a separate validation step is necessary when a calling program finally wants to finish a complete SBML document.

The primary interface to this validation facility is SBMLDocument's SBMLDocument.checkInternalConsistency() and SBMLDocument.checkConsistency(). The former verifies the basic internal consistency and syntax of an SBML document, and the latter implements more elaborate validation rules (both those defined by the SBML specifications, as well as additional rules offered by libSBML).

The checks performed by SBMLDocument.checkInternalConsistency() are hardwired and cannot be changed by calling programs, but the validation performed by SBMLDocument.checkConsistency() is under program control using the method SBMLDocument.setConsistencyChecks(). Applications can selectively disable specific kinds of checks that they may not be interested in, by calling SBMLDocument.setConsistencyChecks() with appropriate parameters.

These methods have slightly different relevance depending on whether a model is created programmaticaly from scratch, or whether it is read in from a file or data stream. The following list summarizes the possible scenarios.

Scenario 1: Creating a model from scratch. Before writing out the model,

Scenario 2: Reading a model from a file or data stream. After reading the model,

  • Basic consistency checks will have been performed automatically by libSBML upon reading the content, so you only need to inquire about the results by using SBMLDocument.getNumErrors()

Converting documents between Levels and Versions of SBML

LibSBML provides facilities for limited translation of SBML between Levels and Versions of the SBML specifications. The method for doing is is setLevelAndVersion() . In general, models can be converted upward without difficulty (e.g., from SBML Level 1 to Level 2, or from an earlier Version of Level 2 to the latest Version of Level 2). Sometimes models can be translated downward as well, if they do not use constructs specific to more advanced Levels of SBML.

Calling SBMLDocument.setLevelAndVersion() will not necessarily lead to a successful conversion. The method will return a boolean value to indicate success or failure. Callers must check the error log (see next section) attached to the SBMLDocument object after calling SBMLDocument.setLevelAndVersion() in order to assess whether any problems arose.

If an application is interested in translating to a lower Level and/or Version of SBML within a Level, the following methods allow for prior assessment of whether there is sufficient compatibility to make a translation possible:

Some changes between Versions of SBML Level 2 may lead to unexpected behaviors when attempting conversions in either direction. For example, SBML Level 2 Version 4 relaxed the requirement for consistency in units of measurement between expressions annd quantities in a model. As a result, a model written in Version 4, if converted to Version 3 with no other changes, may fail validation as a Version 3 model because Version 3 imposed stricter requirements on unit consistency.

Other changes between SBML Level 2 and Level 3 make downward conversions challenging. In some cases, it means that a model converted to Level 2 from Level 3 will contain attributes that were not explicitly given in the Level 3 model, because in Level 2 these attributes may have been optional or have default values.

Error handling

Upon reading a model, SBMLDocument logs any problems encountered while reading the model from the file or data stream. The log contains objects that record diagnostic information about any notable issues that arose. Whether the problems are warnings or errors, they are both reported through a single common interface involving the object class SBMLError.

The methods SBMLDocument.getNumErrors(), SBMLDocument.getError() and SBMLDocument.printErrors() allow callers to interact with the warnings or errors logged. Alternatively, callers may retrieve the entire log as an SBMLErrorLog object using the method SBMLDocument.getErrorLog(). The SBMLErrorLog object provides some alternative methods for interacting with the set of errors and warnings. In either case, applications typically should first call SBMLDocument.getNumErrors() to find out if any issues have been logged after specific libSBML operations such as the ones discussed in the sections above. If they have, then an application will should proceed to inspect the individual reports using either the direct interfaces on SBMLDocument or using the methods on the SBMLErrorLog object.

Public Member Functions

def addCVTerm
 
def appendAnnotation
 
def appendNotes
 
def checkConsistency
 
def checkInternalConsistency
 
def checkL1Compatibility
 
def checkL2v1Compatibility
 
def checkL2v2Compatibility
 
def checkL2v3Compatibility
 
def checkL2v4Compatibility
 
def checkL3v1Compatibility
 
def clone
 
def createModel
 
def disablePackage
 
def enableDefaultNS
 
def enablePackage
 
def expandFunctionDefinitions
 
def expandInitialAssignments
 
def getAncestorOfType
 
def getAnnotation
 
def getAnnotationString
 
def getColumn
 
def getCVTerm
 
def getCVTerms
 
def getDefaultLevel
 
def getDefaultVersion
 
def getElementByMetaId
 
def getElementBySId
 
def getElementName
 
def getError
 
def getErrorLog
 
def getLevel
 
def getLine
 
def getListOfAllElements
 
def getListOfAllElementsFromPlugins
 
def getLocationURI
 
def getMetaId
 
def getModel
 
def getModel
 
def getModelHistory
 
def getNamespaces
 
def getNotes
 
def getNotesString
 
def getNumCVTerms
 
def getNumErrors
 
def getNumPlugins
 
def getPackageName
 
def getPackageRequired
 
def getPackageVersion
 
def getParentSBMLObject
 
def getPkgRequired
 
def getPlugin
 
def getPrefix
 
def getResourceBiologicalQualifier
 
def getResourceModelQualifier
 
def getSBMLDocument
 
def getSBOTerm
 
def getSBOTermAsURL
 
def getSBOTermID
 
def getTypeCode
 
def getURI
 
def getVersion
 
def hasValidLevelVersionNamespaceCombination
 
def isDisabledIgnoredPackage
 
def isEnabledDefaultNS
 
def isIgnoredPackage
 
def isIgnoredPkg
 
def isPackageEnabled
 
def isPackageURIEnabled
 
def isPkgEnabled
 
def isPkgURIEnabled
 
def isSetAnnotation
 
def isSetMetaId
 
def isSetModelHistory
 
def isSetNotes
 
def isSetPackageRequired
 
def isSetPkgRequired
 
def isSetSBOTerm
 
def matchesRequiredSBMLNamespacesForAddition
 
def matchesSBMLNamespaces
 
def printErrors
 
def removeFromParentAndDelete
 
def removeTopLevelAnnotationElement
 
def renameMetaIdRefs
 
def renameSIdRefs
 
def renameUnitSIdRefs
 
def replaceTopLevelAnnotationElement
 
def setAnnotation
 
def setConsistencyChecks
 
def setConsistencyChecksForConversion
 
def setLevelAndVersion
 
def setLocationURI
 
def setMetaId
 
def setModel
 
def setModelHistory
 
def setNamespaces
 
def setNotes
 
def setPackageRequired
 
def setPkgRequired
 
def setSBOTerm
 
def toSBML
 
def toXMLNode
 
def unsetAnnotation
 
def unsetCVTerms
 
def unsetId
 
def unsetMetaId
 
def unsetModelHistory
 
def unsetName
 
def unsetNotes
 
def unsetSBOTerm
 
def validateSBML
 

Member Function Documentation

def libsbml.SBase.addCVTerm (   self,
  args 
)
inherited

Python method signature(s):

addCVTerm(SBase self, CVTerm term, bool newBag=False)   int
addCVTerm(SBase self, CVTerm term)   int

Adds a copy of the given CVTerm object to this SBML object.

Parameters
termthe CVTerm to assign.
newBagif True, creates a new RDF bag with the same identifier as a previous bag, and if False, adds the term to an existing RDF bag with the same type of qualifier as the term being added.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
Since the CV Term uses the 'metaid' attribute of the object as a reference, if the object has no 'metaid' attribute value set, then the CVTerm will not be added.
This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.
Documentation note:
The native C++ implementation of this method defines a default argument value. In the documentation generated for different libSBML language bindings, you may or may not see corresponding arguments in the method declarations. For example, in Java and C#, a default argument is handled by declaring two separate methods, with one of them having the argument and the other one lacking the argument. However, the libSBML documentation will be identical for both methods. Consequently, if you are reading this and do not see an argument even though one is described, please look for descriptions of other variants of this method near where this one appears in the documentation.
def libsbml.SBase.appendAnnotation (   self,
  args 
)
inherited

Python method signature(s):

appendAnnotation(SBase self, XMLNode annotation)   int
appendAnnotation(SBase self, string annotation)   int

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
appendAnnotation(XMLNode annotation)

Appends the given annotation to the 'annotation' subelement of this object.

Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Unlike SBase.setAnnotation() or SBase.setAnnotation(), this method allows other annotations to be preserved when an application adds its own data.

Parameters
annotationan XML structure that is to be copied and appended to the content of the 'annotation' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
getAnnotationString()
isSetAnnotation()
setAnnotation()
setAnnotation()
appendAnnotation()
unsetAnnotation()

Method variant with the following signature:
appendAnnotation(string annotation)

Appends the given annotation to the 'annotation' subelement of this object.

Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Unlike SBase.setAnnotation() or SBase.setAnnotation(), this method allows other annotations to be preserved when an application adds its own data.

Parameters
annotationan XML string that is to be copied and appended to the content of the 'annotation' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
getAnnotationString()
isSetAnnotation()
setAnnotation()
setAnnotation()
appendAnnotation()
unsetAnnotation()
def libsbml.SBase.appendNotes (   self,
  args 
)
inherited

Python method signature(s):

appendNotes(SBase self, XMLNode notes)   int
appendNotes(SBase self, string notes)   int

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
appendNotes(string notes)

Appends the given notes to the 'notes' subelement of this object.

The content of the parameter notes is copied.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

Parameters
notesan XML string that is to appended to the content of the 'notes' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
getNotesString()
isSetNotes()
setNotes()
setNotes()
appendNotes()
unsetNotes()
SyntaxChecker.hasExpectedXHTMLSyntax()

Method variant with the following signature:
appendNotes(XMLNode notes)

Appends the given notes to the 'notes' subelement of this object.

The content of notes is copied.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

Parameters
notesan XML node structure that is to appended to the content of the 'notes' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
getNotesString()
isSetNotes()
setNotes()
setNotes()
appendNotes()
unsetNotes()
SyntaxChecker.hasExpectedXHTMLSyntax()
def libsbml.SBMLDocument.checkConsistency (   self)

Python method signature(s):

checkConsistency(SBMLDocument self)   long

Performs consistency checking and validation on this SBML document.

If this method returns a nonzero value (meaning, one or more consistency checks have failed for SBML document), the failures may be due to warnings or errors. Callers should inspect the severity flag in the individual SBMLError objects returned by SBMLDocument.getError() to determine the nature of the failures.

Returns
the number of failed checks (errors) encountered.
See also
SBMLDocument.checkInternalConsistency()
def libsbml.SBMLDocument.checkInternalConsistency (   self)

Python method signature(s):

checkInternalConsistency(SBMLDocument self)   long

Performs consistency checking on libSBML's internal representation of an SBML Model.

Callers should query the results of the consistency check by calling SBMLDocument.getError().

Returns
the number of failed checks (errors) encountered.

The distinction between this method and SBMLDocument.checkConsistency() is that this method reports on fundamental syntactic and structural errors that violate the XML Schema for SBML; by contrast, SBMLDocument.checkConsistency() performs more elaborate model verifications and also validation according to the validation rules written in the appendices of the SBML Level 2 Versions 2–4 specification documents.

See also
SBMLDocument.checkConsistency()
def libsbml.SBMLDocument.checkL1Compatibility (   self)

Python method signature(s):

checkL1Compatibility(SBMLDocument self)   long

Performs a set of consistency checks on the document to establish whether it is compatible with SBML Level 1 and can be converted to Level 1.

Callers should query the results of the consistency check by calling SBMLDocument.getError().

Returns
the number of failed checks (errors) encountered.
def libsbml.SBMLDocument.checkL2v1Compatibility (   self)

Python method signature(s):

checkL2v1Compatibility(SBMLDocument self)   long

Performs a set of consistency checks on the document to establish whether it is compatible with SBML Level 2 Version 1 and can be converted to Level 2 Version 1.

Callers should query the results of the consistency check by calling SBMLDocument.getError().

Returns
the number of failed checks (errors) encountered.
def libsbml.SBMLDocument.checkL2v2Compatibility (   self)

Python method signature(s):

checkL2v2Compatibility(SBMLDocument self)   long

Performs a set of consistency checks on the document to establish whether it is compatible with SBML Level 2 Version 2 and can be converted to Level 2 Version 2.

Callers should query the results of the consistency check by calling SBMLDocument.getError().

Returns
the number of failed checks (errors) encountered.
def libsbml.SBMLDocument.checkL2v3Compatibility (   self)

Python method signature(s):

checkL2v3Compatibility(SBMLDocument self)   long

Performs a set of consistency checks on the document to establish whether it is compatible with SBML Level 2 Version 3 and can be converted to Level 2 Version 3.

Callers should query the results of the consistency check by calling SBMLDocument.getError().

Returns
the number of failed checks (errors) encountered.
def libsbml.SBMLDocument.checkL2v4Compatibility (   self)

Python method signature(s):

checkL2v4Compatibility(SBMLDocument self)   long

Performs a set of consistency checks on the document to establish whether it is compatible with SBML Level 2 Version 4 and can be converted to Level 2 Version 4.

Callers should query the results of the consistency check by calling SBMLDocument.getError().

Returns
the number of failed checks (errors) encountered.
def libsbml.SBMLDocument.checkL3v1Compatibility (   self)

Python method signature(s):

checkL3v1Compatibility(SBMLDocument self)   long

Performs a set of consistency checks on the document to establish whether it is compatible with SBML Level 3 Version 1 and can be converted to Level 3 Version 1.

Callers should query the results of the consistency check by calling SBMLDocument.getError().

Returns
the number of failed checks (errors) encountered.
def libsbml.SBMLDocument.clone (   self)

Python method signature(s):

clone(SBMLDocument self)   SBMLDocument

Creates and returns a deep copy of this SBMLDocument.

Returns
a (deep) copy of this SBMLDocument.
def libsbml.SBMLDocument.createModel (   self,
  sid = "" 
)

Python method signature(s):

createModel(SBMLDocument self, string sid="")   Model
createModel(SBMLDocument self)   Model

Creates a new Model inside this SBMLDocument, and returns a pointer to it.

In SBML Level 2, the use of an identifier on a Model object is optional. This method takes an optional argument, sid, for setting the identifier. If not supplied, the identifier attribute on the Model instance is not set.

Parameters
sidthe identifier of the new Model to create.
Documentation note:
The native C++ implementation of this method defines a default argument value. In the documentation generated for different libSBML language bindings, you may or may not see corresponding arguments in the method declarations. For example, in Java and C#, a default argument is handled by declaring two separate methods, with one of them having the argument and the other one lacking the argument. However, the libSBML documentation will be identical for both methods. Consequently, if you are reading this and do not see an argument even though one is described, please look for descriptions of other variants of this method near where this one appears in the documentation.
See also
getModel()
SBMLDocument.setModel()
def libsbml.SBase.disablePackage (   self,
  args 
)
inherited

Python method signature(s):

disablePackage(SBase self, string pkgURI, string pkgPrefix)   int

Disables the given SBML Level 3 package on this object.

This method disables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object.

An example of when this may be useful is during construction of model components when mixing existing and new models. Suppose your application read an SBML document containing a model that used the SBML Hierarchical Model Composition (“comp”) package, and extracted parts of that model in order to construct a new model in memory. The new, in-memory model will not accept a component drawn from another SBMLDocument with different package namespace declarations. You could reconstruct the same namespaces in the in-memory model first, but as a shortcut, you could also disable the package namespace on the object being added. Here is a code example to help clarify this:

import sys
import os.path
from libsbml import *

# We read in an SBML L3V1 model that uses the 'comp' package namespace
doc = readSBML('sbml-file-with-comp-elements.xml');

# We extract one of the species from the model we just read in.
s1 = doc.getModel().getSpecies(0);

# We construct a new model.  This model does not use the 'comp' package.
newDoc = SBMLDocument(3, 1);
newModel = newDoc.createModel();

# The following would fail with an error, because addSpecies() would
# first check that the parent of the given object has namespaces
# declared, and will discover that s1 does but newModel does not.

# newModel.addSpecies(s1);

# However, if we disable the 'comp' package on s1, then the call
# to addSpecies will work.

s1.disablePackage('http://www.sbml.org/sbml/level3/version1/comp/version1',
          'comp');
newModel.addSpecies(s1);
Parameters
pkgURIthe URI of the package
pkgPrefixthe XML prefix of the package
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
enablePackage()
def libsbml.SBMLDocument.enableDefaultNS (   self,
  args 
)

Python method signature(s):

enableDefaultNS(SBMLDocument self, string package, bool flag)   int

Set/unset default namespace to each top-level element defined in the given package extension.

This works by adding a xmlns="..." attribute. No prefix will be written when writing elements defined in the given package extension if True is given as second argument.

Parameters
packagethe name or URI of the package extension.
flagboolean value to indicate whether to write a namespace prefix.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.SBase.enablePackage (   self,
  args 
)
inherited

Python method signature(s):

enablePackage(SBase self, string pkgURI, string pkgPrefix, bool flag)   int

Enables or disables the given SBML Level 3 package on this object.

This method enables the specified package on this object and other objects connected by child-parent links in the same SBMLDocument object. This method is the converse of SBase.disablePackage().

Parameters
pkgURIthe URI of the package.
pkgPrefixthe XML prefix of the package
flagwhether to enable (True) or disable (False) the package
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
disablePackage()
def libsbml.SBMLDocument.expandFunctionDefinitions (   self)

Python method signature(s):

expandFunctionDefinitions(SBMLDocument self)   bool

Removes FunctionDefinition constructs from the document and expands any instances of their use within <math> elements.

For example, suppose a Model contains a FunctionDefinition with identifier 'f' representing the math expression: f(x, y) = x * y. Suppose further that there is a reaction in which the <math> element of the KineticLaw object contains f(s, p), where s and p are other identifiers defined in the model. The outcome of invoking this method is that the <math> of the KineticLaw now represents the expression s * p and the model no longer contains any FunctionDefinition objects.

Returns
bool True if the transformation was successful, False, otherwise.
Note
This function will check the consistency of a model before attemptimg the transformation. If the model is not valid SBML, the transformation will not be performed and the function will return false.
def libsbml.SBMLDocument.expandInitialAssignments (   self)

Python method signature(s):

expandInitialAssignments(SBMLDocument self)   bool

Removes InitialAssignment constructs from the document and replaces them with appropriate values.

For example, suppose a Model contains a InitialAssignment to a symbol 'k' where 'k' is the identifier of a Parameter. The outcome of invoking this method is that the 'value' attribute of the Parameter definition is set to the result calculated using the InitialAssignment object's <math> formula, and the corresponding InitialAssignment is then removed from the Model.

Returns
bool True if the transformation was successful, False, otherwise.
Note
This function will check the consistency of a model before attemptimg the transformation. If the model is not valid SBML, the transformation will not be performed and the function will return false. As part of that process, this method will check that it has values for any components referred to by the <math> elements of InitialAssignment objects. In cases where not all of the values have been declared (e.g., if the mathematical expression refers to model entities that have no declared values), the InitialAssignment in question will not be removed and this method will return false.
def libsbml.SBase.getAncestorOfType (   self,
  args 
)
inherited

Python method signature(s):

getAncestorOfType(SBase self, int type, string pkgName="core")   SBase
getAncestorOfType(SBase self, int type)   SBase
getAncestorOfType(SBase self, int type, string pkgName="core")   SBase
getAncestorOfType(SBase self, int type)   SBase

Returns the first ancestor object that has the given SBML type code from the given package.

LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. In the Python language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbml. The names of the type codes all begin with the characters SBML_.

This method searches the tree of objects that are parents of this object, and returns the first one that has the given SBML type code from the given pkgName.

Parameters
typethe SBML type code of the object sought
pkgName(optional) the short name of an SBML Level 3 package to which the sought-after object must belong
Returns
the ancestor SBML object of this SBML object that corresponds to the given SBML object type code, or None if no ancestor exists.
Warning
The optional argument pkgName must be used for all type codes from SBML Level 3 packages. Otherwise, the function will search the 'core' namespace alone, not find any corresponding elements, and return None.
Documentation note:
The native C++ implementation of this method defines a default argument value. In the documentation generated for different libSBML language bindings, you may or may not see corresponding arguments in the method declarations. For example, in Java and C#, a default argument is handled by declaring two separate methods, with one of them having the argument and the other one lacking the argument. However, the libSBML documentation will be identical for both methods. Consequently, if you are reading this and do not see an argument even though one is described, please look for descriptions of other variants of this method near where this one appears in the documentation.
def libsbml.SBase.getAnnotation (   self,
  args 
)
inherited

Python method signature(s):

getAnnotation(SBase self)   XMLNode
getAnnotation(SBase self)   XMLNode

Returns the content of the 'annotation' subelement of this object as a tree of XMLNode objects.

Whereas the SBML 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

The annotations returned by this method will be in XML form. LibSBML provides an object model and related interfaces for certain specific kinds of annotations, namely model history information and RDF content. See the ModelHistory, CVTerm and RDFAnnotationParser classes for more information about the facilities available.

Returns
the annotation of this SBML object as a tree of XMLNode objects.
See also
getAnnotationString()
isSetAnnotation()
setAnnotation()
setAnnotation()
appendAnnotation()
appendAnnotation()
unsetAnnotation()
def libsbml.SBase.getAnnotationString (   self,
  args 
)
inherited

Python method signature(s):

getAnnotationString(SBase self)   string
getAnnotationString(SBase self)   string

Returns the content of the 'annotation' subelement of this object as a character string.

Whereas the SBML 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

The annotations returned by this method will be in string form. See the method getAnnotation() for a version that returns annotations in XML form.

Returns
the annotation of this SBML object as a character string.
See also
getAnnotation()
isSetAnnotation()
setAnnotation()
setAnnotation()
appendAnnotation()
appendAnnotation()
unsetAnnotation()
def libsbml.SBase.getColumn (   self)
inherited

Python method signature(s):

getColumn(SBase self)   long

Returns the column number on which this object first appears in the XML representation of the SBML document.

Returns
the column number of this SBML object.
Note
The column number for each construct in an SBML model is set upon reading the model. The accuracy of the column number depends on the correctness of the XML representation of the model, and on the particular XML parser library being used. The former limitation relates to the following problem: if the model is actually invalid XML, then the parser may not be able to interpret the data correctly and consequently may not be able to establish the real column number. The latter limitation is simply that different parsers seem to have their own accuracy limitations, and out of all the parsers supported by libSBML, none have been 100% accurate in all situations. (At this time, libSBML supports the use of libxml2, Expat and Xerces.)
See also
getLine()
def libsbml.SBase.getCVTerm (   self,
  args 
)
inherited

Python method signature(s):

getCVTerm(SBase self, long n)   CVTerm

Returns the nth CVTerm in the list of CVTerms of this SBML object.

Parameters
nlong the index of the CVTerm to retrieve
Returns
the nth CVTerm in the list of CVTerms for this SBML object.
def libsbml.SBase.getCVTerms (   self)
inherited

Python method signature(s):

getCVTerms()   CVTermList

Get the CVTermList of CVTerm objects in this SBase.

Returns the CVTermList for this SBase.

def libsbml.SBMLDocument.getDefaultLevel ( )

{core}

Container for an SBML document and interface for global operations on SBML documents.

LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). The two primary means of reading an SBML model, SBMLReader.readSBML() and SBMLReader.readSBMLFromString(), both return a pointer to an SBMLDocument object. From there, callers can inquire about any errors encountered (e.g., using SBMLDocument.getNumErrors()), access the Model object, and perform other actions such as consistency-checking and model translation.

When creating fresh models programmatically, the starting point is typically the creation of an SBMLDocument object instance. The SBMLDocument constructor accepts arguments for the SBML Level and Version of the model to be created. After creating the SBMLDocument object, calling programs then typically call SBMLDocument.createModel() almost immediately, and then proceed to call the methods on the Model object to fill out the model's contents.

SBMLDocument corresponds roughly to the class Sbml defined in the SBML Level 2 specification and SBML in the Level 3 specification. It does not have a direct correspondence in SBML Level 1. (However, to make matters simpler for applications, libSBML creates an SBMLDocument no matter whether the model is Level 1, Level 2 or Level 3.) In its barest form, when written out in XML format for (e.g.) SBML Level 2 Version 4, the corresponding structure is the following:

<sbml xmlns='http://www.sbml.org/sbml/level2/version4' level='2' version='4'>
  ...
</sbml>

SBMLDocument is derived from SBase, and therefore contains the usual SBase attributes (in SBML Level 2 and Level 3) of 'metaid' and 'sboTerm', as well as the subelements 'notes' and 'annotation'. It also contains the attributes 'level' and 'version' indicating the Level and Version of the SBML data structure. These can be accessed using the methods defined by the SBase class for that purpose.

Consistency and adherence to SBML specifications

One of the most important features of libSBML is its ability to perform SBML validation to ensure that a model adheres to the SBML specification for whatever Level+Version combination the model uses. SBMLDocument provides the methods for running consistency-checking and validation rules on the SBML content.

First, a brief explanation of the rationale is in order. In libSBML versions up to and including the version 3.3.x series, the individual methods for creating and setting attributes and other components were quite lenient, and allowed a caller to compose SBML entities that might not, in the end, represent valid SBML. This allowed applications the freedom to do things such as save incomplete models (which is useful when models are being developed over long periods of time). In the version 4.x series, libSBML is somewhat stricter, but still permits structures to be created independently and the results to be combined in a separate step. In all these cases, it means that a separate validation step is necessary when a calling program finally wants to finish a complete SBML document.

The primary interface to this validation facility is SBMLDocument's SBMLDocument.checkInternalConsistency() and SBMLDocument.checkConsistency(). The former verifies the basic internal consistency and syntax of an SBML document, and the latter implements more elaborate validation rules (both those defined by the SBML specifications, as well as additional rules offered by libSBML).

The checks performed by SBMLDocument.checkInternalConsistency() are hardwired and cannot be changed by calling programs, but the validation performed by SBMLDocument.checkConsistency() is under program control using the method SBMLDocument.setConsistencyChecks(). Applications can selectively disable specific kinds of checks that they may not be interested in, by calling SBMLDocument.setConsistencyChecks() with appropriate parameters.

These methods have slightly different relevance depending on whether a model is created programmaticaly from scratch, or whether it is read in from a file or data stream. The following list summarizes the possible scenarios.

Scenario 1: Creating a model from scratch. Before writing out the model,

Scenario 2: Reading a model from a file or data stream. After reading the model,

  • Basic consistency checks will have been performed automatically by libSBML upon reading the content, so you only need to inquire about the results by using SBMLDocument.getNumErrors()

Converting documents between Levels and Versions of SBML

LibSBML provides facilities for limited translation of SBML between Levels and Versions of the SBML specifications. The method for doing is is setLevelAndVersion() . In general, models can be converted upward without difficulty (e.g., from SBML Level 1 to Level 2, or from an earlier Version of Level 2 to the latest Version of Level 2). Sometimes models can be translated downward as well, if they do not use constructs specific to more advanced Levels of SBML.

Calling SBMLDocument.setLevelAndVersion() will not necessarily lead to a successful conversion. The method will return a boolean value to indicate success or failure. Callers must check the error log (see next section) attached to the SBMLDocument object after calling SBMLDocument.setLevelAndVersion() in order to assess whether any problems arose.

If an application is interested in translating to a lower Level and/or Version of SBML within a Level, the following methods allow for prior assessment of whether there is sufficient compatibility to make a translation possible:

Some changes between Versions of SBML Level 2 may lead to unexpected behaviors when attempting conversions in either direction. For example, SBML Level 2 Version 4 relaxed the requirement for consistency in units of measurement between expressions annd quantities in a model. As a result, a model written in Version 4, if converted to Version 3 with no other changes, may fail validation as a Version 3 model because Version 3 imposed stricter requirements on unit consistency.

Other changes between SBML Level 2 and Level 3 make downward conversions challenging. In some cases, it means that a model converted to Level 2 from Level 3 will contain attributes that were not explicitly given in the Level 3 model, because in Level 2 these attributes may have been optional or have default values.

Error handling

Upon reading a model, SBMLDocument logs any problems encountered while reading the model from the file or data stream. The log contains objects that record diagnostic information about any notable issues that arose. Whether the problems are warnings or errors, they are both reported through a single common interface involving the object class SBMLError.

The methods SBMLDocument.getNumErrors(), SBMLDocument.getError() and SBMLDocument.printErrors() allow callers to interact with the warnings or errors logged. Alternatively, callers may retrieve the entire log as an SBMLErrorLog object using the method SBMLDocument.getErrorLog(). The SBMLErrorLog object provides some alternative methods for interacting with the set of errors and warnings. In either case, applications typically should first call SBMLDocument.getNumErrors() to find out if any issues have been logged after specific libSBML operations such as the ones discussed in the sections above. If they have, then an application will should proceed to inspect the individual reports using either the direct interfaces on SBMLDocument or using the methods on the SBMLErrorLog object. Python method signature(s):

getDefaultLevel()   long

The default SBML Level of new SBMLDocument objects.

This 'default Level' corresponds to the most recent SBML specification Level available at the time libSBML version 5.10.0 was released. The default Level is used by SBMLDocument if no Level is explicitly specified at the time of the construction of an SBMLDocument instance.
Returns
an integer indicating the most recent SBML specification Level
Note
Because this is a static method on a class, the Python language interface for libSBML will contain two variants. One will be the expected, normal static method on the class (i.e., a regular methodName), and the other will be a standalone top-level function with the name ClassName_methodName(). This is merely an artifact of how the language interfaces are created in libSBML. The methods are functionally identical.
See also
SBMLDocument.getDefaultVersion()
def libsbml.SBMLDocument.getDefaultVersion ( )

Python method signature(s):

getDefaultVersion()   long

The default Version of new SBMLDocument objects.

This 'default Version' corresponds to the most recent Version within the most recent Level of SBML available at the time libSBML version 5.10.0 was released. The default Version is used by SBMLDocument if no Version is explicitly specified at the time of the construction of an SBMLDocument instance.
Returns
an integer indicating the most recent SBML specification Version
Note
Because this is a static method on a class, the Python language interface for libSBML will contain two variants. One will be the expected, normal static method on the class (i.e., a regular methodName), and the other will be a standalone top-level function with the name ClassName_methodName(). This is merely an artifact of how the language interfaces are created in libSBML. The methods are functionally identical.
See also
SBMLDocument.getDefaultLevel()
def libsbml.SBMLDocument.getElementByMetaId (   self,
  args 
)

Python method signature(s):

getElementByMetaId(SBMLDocument self, string metaid)   SBase

Returns the first child element it can find with the given metaid, or itself if it has the given metaid, or None if no such object is found.

Parameters
metaidstring representing the metaid of objects to find
Returns
pointer to the first element found with the given metaid.
def libsbml.SBMLDocument.getElementBySId (   self,
  args 
)

Python method signature(s):

getElementBySId(SBMLDocument self, string id)   SBase

Returns the first child element found that has the given id in the model-wide SId namespace, or None if no such object is found.

Parameters
idstring representing the id of objects to find
Returns
pointer to the first element found with the given id.
def libsbml.SBMLDocument.getElementName (   self)

Python method signature(s):

getElementName(SBMLDocument self)   string

Returns the XML element name of this object, which for SBMLDocument, is always 'sbml'.

Returns
the name of this element, i.e., 'sbml'.
def libsbml.SBMLDocument.getError (   self,
  args 
)

Python method signature(s):

getError(SBMLDocument self, long n)   SBMLError

Returns the nth error or warning encountered during parsing, consistency checking, or attempted translation of this model.

Callers can use method XMLError.getSeverity() on the result to assess the severity of the problem. The possible severity levels range from informational messages to fatal errors.

Returns
the error or warning indexed by integer n, or return None if n > (getNumErrors() - 1).
Parameters
nthe integer index of the error sought.
See also
SBMLDocument.getNumErrors()
def libsbml.SBMLDocument.getErrorLog (   self,
  args 
)

Python method signature(s):

getErrorLog(SBMLDocument self)   SBMLErrorLog
getErrorLog(SBMLDocument self)   SBMLErrorLog

Returns the list of errors or warnings logged during parsing, consistency checking, or attempted translation of this model.

Returns
the SBMLErrorLog used for this SBMLDocument
See also
SBMLDocument.getNumErrors()
def libsbml.SBase.getLevel (   self)
inherited

Python method signature(s):

getLevel(SBase self)   long

Returns the SBML Level of the SBMLDocument object containing this object.

LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)
Returns
the SBML level of this SBML object.
See also
getVersion()
getNamespaces()
getPackageVersion()
def libsbml.SBase.getLine (   self)
inherited

Python method signature(s):

getLine(SBase self)   long

Returns the line number on which this object first appears in the XML representation of the SBML document.

Returns
the line number of this SBML object.
Note
The line number for each construct in an SBML model is set upon reading the model. The accuracy of the line number depends on the correctness of the XML representation of the model, and on the particular XML parser library being used. The former limitation relates to the following problem: if the model is actually invalid XML, then the parser may not be able to interpret the data correctly and consequently may not be able to establish the real line number. The latter limitation is simply that different parsers seem to have their own accuracy limitations, and out of all the parsers supported by libSBML, none have been 100% accurate in all situations. (At this time, libSBML supports the use of libxml2, Expat and Xerces.)
See also
getColumn()
def libsbml.SBase.getListOfAllElements (   self,
  filter = None 
)
inherited

Python method signature(s):

getListOfAllElements(SBase self, ElementFilter filter=None)   SBaseList
getListOfAllElements(SBase self)   SBaseList

Returns an SBaseList of all child SBase objects, including those nested to an arbitrary depth.

Returns
an SBaseList
def libsbml.SBase.getListOfAllElementsFromPlugins (   self,
  filter = None 
)
inherited

Python method signature(s):

getListOfAllElementsFromPlugins(SBase self, ElementFilter filter=None)   SBaseList
getListOfAllElementsFromPlugins(SBase self)   SBaseList

Returns an SBaseList of all child SBase objects contained in SBML package plugins.

This method walks down the list of all packages used by the model and returns all objects contained in them.

Returns
an SBaseList of all children objects from plugins.
def libsbml.SBMLDocument.getLocationURI (   self,
  args 
)

Python method signature(s):

getLocationURI(SBMLDocument self)   string
getLocationURI(SBMLDocument self)   string

Get the location of this SBMLDocument.

If this document was read from a file or had its location set manually, that filename or set location will be returned, otherwise, an empty string is returned.

def libsbml.SBase.getMetaId (   self)
inherited

Python method signature(s):

getMetaId(SBase self)   string

Returns the value of the 'metaid' attribute of this object.

The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use the XML ID type. Although SBML itself specifies the use of XML ID only for the 'metaid' attribute, SBML-compatible applications should be careful if they use XML ID's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.
Returns
the meta-identifier of this SBML object.
See also
isSetMetaId()
setMetaId()
def libsbml.SBase.getModel (   self)
inherited

Python method signature(s):

getModel(SBase self)   Model

Returns the Model object for the SBML Document in which the current object is located.

Returns
the Model object for the SBML Document of this SBML object.
See also
getParentSBMLObject()
getSBMLDocument()
def libsbml.SBMLDocument.getModel (   self,
  args 
)

Python method signature(s):

getModel(SBMLDocument self)   Model
getModel(SBMLDocument self)   Model

Returns the Model object stored in this SBMLDocument.

It is important to note that this method does not create a Model instance. The model in the SBMLDocument must have been created at some prior time, for example using SBMLDocument.createModel() or SBMLDocument.setModel(). This method returns None if a model does not yet exist.

Returns
the Model contained in this SBMLDocument.
See also
createModel()
def libsbml.SBase.getModelHistory (   self,
  args 
)
inherited

Python method signature(s):

getModelHistory(SBase self)   ModelHistory
getModelHistory(SBase self)   ModelHistory

Returns the ModelHistory object, if any, attached to this object.

Returns
the ModelHistory object attached to this object, or None if none exist.
Note
In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.
def libsbml.SBMLDocument.getNamespaces (   self)

Python method signature(s):

getNamespaces(SBMLDocument self)   XMLNamespaces

Returns a list of XML Namespaces associated with the XML content of this SBML document.

Returns
the XML Namespaces associated with this SBML object
def libsbml.SBase.getNotes (   self,
  args 
)
inherited

Python method signature(s):

getNotes(SBase self)   XMLNode
getNotes(SBase self)   XMLNode

Returns the content of the 'notes' subelement of this object as a tree of XMLNode objects.

The optional SBML element named 'notes', present on every major SBML component type (and in SBML Level 3, the 'message' subelement of Constraint), is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements conform to the definition of XHTML 1.0. However, the content cannot be entirely free-form; it must satisfy certain requirements defined in the SBML specifications for specific SBML Levels. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); The method implements a verification process that lets callers check whether the content of a given XMLNode object conforms to the SBML requirements for 'notes' and 'message' structure. Developers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations of using 'notes' in SBML. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

The 'notes' element content returned by this method will be in XML form, but libSBML does not provide an object model specifically for the content of notes. Callers will need to traverse the XML tree structure using the facilities available on XMLNode and related objects. For an alternative method of accessing the notes, see getNotesString().

Returns
the content of the 'notes' subelement of this SBML object as a tree structure composed of XMLNode objects.
See also
getNotesString()
isSetNotes()
setNotes()
setNotes()
appendNotes()
appendNotes()
unsetNotes()
SyntaxChecker.hasExpectedXHTMLSyntax()
def libsbml.SBase.getNotesString (   self,
  args 
)
inherited

Python method signature(s):

getNotesString(SBase self)   string
getNotesString(SBase self)   string

Returns the content of the 'notes' subelement of this object as a string.

The optional SBML element named 'notes', present on every major SBML component type (and in SBML Level 3, the 'message' subelement of Constraint), is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements conform to the definition of XHTML 1.0. However, the content cannot be entirely free-form; it must satisfy certain requirements defined in the SBML specifications for specific SBML Levels. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); The method implements a verification process that lets callers check whether the content of a given XMLNode object conforms to the SBML requirements for 'notes' and 'message' structure. Developers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations of using 'notes' in SBML. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

For an alternative method of accessing the notes, see getNotes(), which returns the content as an XMLNode tree structure. Depending on an application's needs, one or the other method may be more convenient.

Returns
the content of the 'notes' subelement of this SBML object as a string.
See also
getNotes()
isSetNotes()
setNotes()
setNotes()
appendNotes()
appendNotes()
unsetNotes()
SyntaxChecker.hasExpectedXHTMLSyntax()
def libsbml.SBase.getNumCVTerms (   self)
inherited

Python method signature(s):

getNumCVTerms(SBase self)   long

Returns the number of CVTerm objects in the annotations of this SBML object.

Returns
the number of CVTerms for this SBML object.
def libsbml.SBMLDocument.getNumErrors (   self,
  args 
)

Python method signature(s):

getNumErrors(SBMLDocument self)   long
getNumErrors(SBMLDocument self, long severity)   long

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
getNumErrors(long severity)

Returns the number of errors or warnings encountered with the given severity during parsing, consistency checking, or attempted translation of this model.

Parameters
severitythe severity of the error sought.
Returns
the number of errors or warnings encountered
See also
SBMLDocument.getError()

Method variant with the following signature:
getNumErrors()

Returns the number of errors or warnings encountered during parsing, consistency checking, or attempted translation of this model.

Returns
the number of errors or warnings encountered
See also
SBMLDocument.getError()
def libsbml.SBase.getNumPlugins (   self)
inherited

Python method signature(s):

getNumPlugins(SBase self)   long

Returns the number of plug-in objects (extenstion interfaces) for SBML Level 3 package extensions known.

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
Returns
the number of plug-in objects (extension interfaces) of package extensions known by this instance of libSBML.
def libsbml.SBase.getPackageName (   self)
inherited

Python method signature(s):

getPackageName(SBase self)   string

Returns the name of the SBML Level 3 package in which this element is defined.

Returns
the name of the SBML package in which this element is defined. The string "core" will be returned if this element is defined in SBML Level 3 Core. The string "unknown" will be returned if this element is not defined in any SBML package.
def libsbml.SBMLDocument.getPackageRequired (   self,
  args 
)

Python method signature(s):

getPackageRequired(SBMLDocument self, string package)   bool

Returns the required attribute of the given package extension.

Note
The name of package must not be given if the package is not enabled.
Parameters
packagethe name or URI of the package extension.
Returns
Boolean flag indicating whether the package is flagged as being required.
def libsbml.SBase.getPackageVersion (   self)
inherited

Python method signature(s):

getPackageVersion(SBase self)   long

Returns the Version of the SBML Level 3 package to which this element belongs to.

Returns
the version of the SBML Level 3 package to which this element belongs. The value 0 will be returned if this element belongs to the SBML Level 3 Core package.
See also
getLevel()
getVersion()
def libsbml.SBase.getParentSBMLObject (   self,
  args 
)
inherited

Python method signature(s):

getParentSBMLObject(SBase self)   SBase
getParentSBMLObject(SBase self)   SBase

Returns the parent SBML object containing this object.

This returns the immediately-containing object. This method is convenient when holding an object nested inside other objects in an SBML model.

Returns
the parent SBML object of this SBML object.
See also
getSBMLDocument()
getModel()
def libsbml.SBMLDocument.getPkgRequired (   self,
  args 
)

Python method signature(s):

getPkgRequired(SBMLDocument self, string package)   bool

Returns the required attribute of the given package extension.

Note
The name of package must not be given if the package is not enabled.
Parameters
packagethe name or URI of the package extension.
Returns
a Boolean value indicating whether the package is flagged as being required in this SBML document.
def libsbml.SBase.getPlugin (   self,
  args 
)
inherited

Python method signature(s):

getPlugin(SBase self, string package)   SBasePlugin
getPlugin(SBase self, string package)   SBasePlugin
getPlugin(SBase self, long n)   SBasePlugin
getPlugin(SBase self, long n)   SBasePlugin

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
getPlugin(long n)

Returns the nth plug-in object (extension interface) for an SBML Level 3 package extension.

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
Parameters
nthe index of the plug-in to return
Returns
the plug-in object (the libSBML extension interface) of a package extension with the given package name or URI.

Method variant with the following signature:
getPlugin(string package)

Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given package name or URI.

SBML Level 3 consists of a Core definition that can be extended via optional SBML Level 3 packages. A given model may indicate that it uses one or more SBML packages, and likewise, a software tool may be able to support one or more packages. LibSBML does not come preconfigured with all possible packages included and enabled, in part because not all package specifications have been finalized. To support the ability for software systems to enable support for the Level 3 packages they choose, libSBML features a plug-in mechanism. Each SBML Level 3 package is implemented in a separate code plug-in that can be enabled by the application to support working with that SBML package. A given SBML model may thus contain not only objects defined by SBML Level 3 Core, but also objects created by libSBML plug-ins supporting additional Level 3 packages.
Parameters
packagethe name or URI of the package
Returns
the plug-in object (the libSBML extension interface) of a package extension with the given package name or URI.
def libsbml.SBase.getPrefix (   self)
inherited

Python method signature(s):

getPrefix(SBase self)   string

Returns the namespace prefix of this element.

def libsbml.SBase.getResourceBiologicalQualifier (   self,
  args 
)
inherited

Python method signature(s):

getResourceBiologicalQualifier(SBase self, string resource)   long

Returns the MIRIAM biological qualifier associated with the given resource.

In MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The latter kind is used to qualify the relationship between a model component and a biological entity which it represents. Examples of relationships include 'is' and 'has part', but many others are possible. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify biological annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM biological qualifiers are represented using valueswhose names begin with BQB_ in the interface class libsbml.

This method searches the controlled-vocabulary annotations (i.e., the list of CVTerm objects) on the present object, then out of those that have biological qualifiers, looks for an annotation to the given resource. If such an annotation is found, it returns the type of biological qualifier associated with that resource as a valuewhose name begins with BQB_ from the interface class libsbml.

Parameters
resourcestring representing the resource; e.g., 'http://www.geneontology.org/#GO:0005892'.
Returns
the qualifier associated with the resource, or BQB_UNKNOWN if the resource does not exist.
Note
The set of MIRIAM biological qualifiers grows over time, although relatively slowly. The values are up to date with MIRIAM at the time of a given libSBML release. The set of values in list of BQB_ constants defined in libsbml may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.
def libsbml.SBase.getResourceModelQualifier (   self,
  args 
)
inherited

Python method signature(s):

getResourceModelQualifier(SBase self, string resource)   long

Returns the MIRIAM model qualifier associated with the given resource.

In MIRIAM, qualifiers are an optional means of indicating the relationship between a model component and its annotations. There are two broad kinds of annotations: model and biological. The former kind is used to qualify the relationship between a model component and another modeling object. An example qualifier is 'isDerivedFrom', to indicate that a given component of the model is derived from the modeling object represented by the referenced resource. MIRIAM defines numerous relationship qualifiers to enable different software tools to qualify model annotations in the same standardized way. In libSBML, the MIRIAM controlled-vocabulary annotations on an SBML model element are represented using lists of CVTerm objects, and the the MIRIAM model qualifiers are represented using valueswhose names begin with BQM_ in the interface class libsbml.

This method method searches the controlled-vocabulary annotations (i.e., the list of CVTerm objects) on the present object, then out of those that have model qualifiers, looks for an annotation to the given resource. If such an annotation is found, it returns the type of type of model qualifier associated with that resource as a valuewhose name begins with BQM_ from the interface class libsbml.

Parameters
resourcestring representing the resource; e.g., 'http://www.geneontology.org/#GO:0005892'.
Returns
the model qualifier type associated with the resource, or BQM_UNKNOWN if the resource does not exist.
Note
The set of MIRIAM model qualifiers grows over time, although relatively slowly. The values are up to date with MIRIAM at the time of a given libSBML release. The set of values in list of BQM_ constants defined in libsbml may be expanded in later libSBML releases, to match the values defined by MIRIAM at that later time.
def libsbml.SBase.getSBMLDocument (   self,
  args 
)
inherited

Python method signature(s):

getSBMLDocument(SBase self)   SBMLDocument
getSBMLDocument(SBase self)   SBMLDocument

Returns the SBMLDocument object containing this object instance.

LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)

This method allows the caller to obtain the SBMLDocument for the current object.

Returns
the parent SBMLDocument object of this SBML object.
See also
getParentSBMLObject()
getModel()
def libsbml.SBase.getSBOTerm (   self)
inherited

Python method signature(s):

getSBOTerm(SBase self)   int

Returns the integer portion of the value of the 'sboTerm' attribute of this object.

Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers. (For convenience, libSBML offers methods for returning both the integer form and a text-string form of the SBO identifier.)

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.

Returns
the value of the 'sboTerm' attribute as an integer, or -1 if the value is not set.
def libsbml.SBase.getSBOTermAsURL (   self)
inherited

Python method signature(s):

getSBOTermAsURL(SBase self)   string

Returns the identifiers.org URL representation of the 'sboTerm' attribute of this object.

This method returns the entire SBO identifier as a text string in the form 'http://identifiers.org/biomodels.sbo/SBO:NNNNNNN'.

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.

Returns
the value of the 'sboTerm' attribute as an identifiers.org URL (its value will be of the form 'http://identifiers.org/biomodels.sbo/SBO:NNNNNNN'), or an empty string if the value is not set.
def libsbml.SBase.getSBOTermID (   self)
inherited

Python method signature(s):

getSBOTermID(SBase self)   string

Returns the string representation of the 'sboTerm' attribute of this object.

Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers. This method returns the entire SBO identifier as a text string in the form 'SBO:NNNNNNN'.

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.

Returns
the value of the 'sboTerm' attribute as a string (its value will be of the form 'SBO:NNNNNNN'), or an empty string if the value is not set.
def libsbml.SBMLDocument.getTypeCode (   self)

Python method signature(s):

getTypeCode(SBMLDocument self)   int

Returns the libSBML type code for this SBML object.

LibSBML attaches an identifying code to every kind of SBML object. These are integer constants known as SBML type codes. The names of all the codes begin with the characters “SBML_”. In the Python language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbml. Note that different Level 3 package plug-ins may use overlapping type codes; to identify the package to which a given object belongs, call the getPackageName() method on the object.
Returns
the SBML type code for this object: SBML_DOCUMENT (default).
Warning
The specific integer values of the possible type codes may be reused by different Level 3 package plug-ins. Thus, to identifiy the correct code, it is necessary to invoke both getTypeCode() and getPackageName().
See also
SBMLDocument.getElementName()
getPackageName()
def libsbml.SBase.getURI (   self)
inherited

Python method signature(s):

getURI(SBase self)   string

Gets the namespace URI to which this element belongs to.

For example, all elements that belong to SBML Level 3 Version 1 Core must would have the URI 'http://www.sbml.org/sbml/level3/version1/core'; all elements that belong to Layout Extension Version 1 for SBML Level 3 Version 1 Core must would have the URI 'http://www.sbml.org/sbml/level3/version1/layout/version1/'

This function first returns the URI for this element by looking into the SBMLNamespaces object of the document with the its package name. If not found, it willreturn the XML namespace to which this element belongs.

Returns
the URI of this element
See also
getSBMLDocument()
getPackageName()
def libsbml.SBase.getVersion (   self)
inherited

Python method signature(s):

getVersion(SBase self)   long

Returns the Version within the SBML Level of the SBMLDocument object containing this object.

LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)
Returns
the SBML version of this SBML object.
See also
getLevel()
getNamespaces()
def libsbml.SBase.hasValidLevelVersionNamespaceCombination (   self)
inherited

Python method signature(s):

hasValidLevelVersionNamespaceCombination(SBase self)   bool
def libsbml.SBMLDocument.isDisabledIgnoredPackage (   self,
  args 
)

Python method signature(s):

isDisabledIgnoredPackage(SBMLDocument self, string pkgURI)   bool

Returns True if the given package extension is one of an ignored packages that has been disabled, otherwise returns False.

An ignored package is one that is defined to be used in this SBML document, but the package is not enabled in this copy of libSBML. It may have been disabled to avoid reproducing the package information when writing out the file.

Parameters
pkgURIthe URI of the package extension.
Returns
a Boolean, True if the package is being ignored and False otherwise.
def libsbml.SBMLDocument.isEnabledDefaultNS (   self,
  args 
)

Python method signature(s):

isEnabledDefaultNS(SBMLDocument self, string package)   bool

Returns True if a default namespace is added to each top-level element defined in the given package extension, otherwise returns False.

This basically checks if the attribute xmlns="..." is present.

Parameters
packagethe name or URI of the package extension.
Returns
a boolean
def libsbml.SBMLDocument.isIgnoredPackage (   self,
  args 
)

Python method signature(s):

isIgnoredPackage(SBMLDocument self, string pkgURI)   bool

Returns True if the given package extension is one of an ignored packages, otherwise returns False.

An ignored package is one that is defined to be used in this SBML document, but the package is not enabled in this copy of libSBML.

Parameters
pkgURIthe URI of the package extension.
Returns
a Boolean, True if the package is being ignored and False otherwise.
def libsbml.SBMLDocument.isIgnoredPkg (   self,
  args 
)

Python method signature(s):

isIgnoredPkg(SBMLDocument self, string pkgURI)   bool

Returns True if the given package extension is one of ignored packages, otherwise returns False.

An ignored package is one that is defined to be used in this SBML document, but the package is not enabled in this copy of libSBML.

Parameters
pkgURIthe URI of the package extension.
Returns
a boolean
def libsbml.SBase.isPackageEnabled (   self,
  args 
)
inherited

Python method signature(s):

isPackageEnabled(SBase self, string pkgName)   bool

Predicate returning True if the given SBML Level 3 package is enabled with this object.

The search ignores the package version.

Parameters
pkgNamethe name of the package
Returns
True if the given package is enabled within this object, false otherwise.
See also
isPackageURIEnabled()
def libsbml.SBase.isPackageURIEnabled (   self,
  args 
)
inherited

Python method signature(s):

isPackageURIEnabled(SBase self, string pkgURI)   bool

Predicate returning True if an SBML Level 3 package with the given URI is enabled with this object.

Parameters
pkgURIthe URI of the package
Returns
True if the given package is enabled within this object, false otherwise.
See also
isPackageEnabled()
def libsbml.SBase.isPkgEnabled (   self,
  args 
)
inherited

Python method signature(s):

isPkgEnabled(SBase self, string pkgName)   bool

Predicate returning True if the given SBML Level 3 package is enabled with this object.

The search ignores the package version.

Parameters
pkgNamethe name of the package
Returns
True if the given package is enabled within this object, false otherwise.
See also
isPkgURIEnabled()
def libsbml.SBase.isPkgURIEnabled (   self,
  args 
)
inherited

Python method signature(s):

isPkgURIEnabled(SBase self, string pkgURI)   bool

Predicate returning True if an SBML Level 3 package with the given URI is enabled with this object.

Parameters
pkgURIthe URI of the package
Returns
True if the given package is enabled within this object, false otherwise.
See also
isPkgEnabled()
def libsbml.SBase.isSetAnnotation (   self)
inherited

Python method signature(s):

isSetAnnotation(SBase self)   bool

Predicate returning True if this object's 'annotation' subelement exists and has content.

Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Returns
True if a 'annotation' subelement exists, False otherwise.
See also
getAnnotation()
getAnnotationString()
setAnnotation()
setAnnotation()
appendAnnotation()
appendAnnotation()
unsetAnnotation()
def libsbml.SBase.isSetMetaId (   self)
inherited

Python method signature(s):

isSetMetaId(SBase self)   bool

Predicate returning True if this object's 'metaid' attribute is set.

The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use the XML ID type. Although SBML itself specifies the use of XML ID only for the 'metaid' attribute, SBML-compatible applications should be careful if they use XML ID's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.
Returns
True if the 'metaid' attribute of this SBML object is set, False otherwise.
See also
getMetaId()
setMetaId()
def libsbml.SBase.isSetModelHistory (   self)
inherited

Python method signature(s):

isSetModelHistory(SBase self)   bool

Predicate returning True if this object has a ModelHistory object attached to it.

Returns
True if the ModelHistory of this object is set, false otherwise.
Note
In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.
def libsbml.SBase.isSetNotes (   self)
inherited

Python method signature(s):

isSetNotes(SBase self)   bool

Predicate returning True if this object's 'notes' subelement exists and has content.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

Returns
True if a 'notes' subelement exists, False otherwise.
See also
getNotes()
getNotesString()
setNotes()
setNotes()
appendNotes()
appendNotes()
unsetNotes()
SyntaxChecker.hasExpectedXHTMLSyntax()
def libsbml.SBMLDocument.isSetPackageRequired (   self,
  args 
)

Python method signature(s):

isSetPackageRequired(SBMLDocument self, string package)   bool

Returns True if the required attribute of the given package extension is defined, otherwise returns False.

Note
The name of package must not be given if the package is not enabled.
Parameters
packagethe name or URI of the package extension.
Returns
a Boolean
def libsbml.SBMLDocument.isSetPkgRequired (   self,
  args 
)

Python method signature(s):

isSetPkgRequired(SBMLDocument self, string package)   bool

Returns True if the required attribute of the given package extension is defined, otherwise returns False.

Note
The name of package must not be given if the package is not enabled.
Parameters
packagethe name or URI of the package extension.
Returns
a Boolean value.
def libsbml.SBase.isSetSBOTerm (   self)
inherited

Python method signature(s):

isSetSBOTerm(SBase self)   bool

Predicate returning True if this object's 'sboTerm' attribute is set.

Returns
True if the 'sboTerm' attribute of this SBML object is set, False otherwise.
def libsbml.SBase.matchesRequiredSBMLNamespacesForAddition (   self,
  args 
)
inherited

Python method signature(s):

matchesRequiredSBMLNamespacesForAddition(SBase self, SBase sb)   bool
matchesRequiredSBMLNamespacesForAddition(SBase self, SBase sb)   bool

Returns True if this object's set of XML namespaces are a subset of the given object's XML namespaces.

The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core. A common approach to using libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.
Parameters
sban object to compare with respect to namespaces
Returns
boolean, True if this object's collection of namespaces is a subset of sb's, False otherwise.
def libsbml.SBase.matchesSBMLNamespaces (   self,
  args 
)
inherited

Python method signature(s):

matchesSBMLNamespaces(SBase self, SBase sb)   bool
matchesSBMLNamespaces(SBase self, SBase sb)   bool

Returns True if this object's set of XML namespaces are the same as the given object's XML namespaces.

The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core. A common approach to using libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.
Parameters
sban object to compare with respect to namespaces
Returns
boolean, True if this object's collection of namespaces is the same as sb's, False otherwise.
def libsbml.SBMLDocument.printErrors (   self,
  args 
)

Python method signature(s):

printErrors(SBMLDocument self, ostream stream=cerr)
printErrors(SBMLDocument self)

Prints all the errors or warnings encountered trying to parse, check, or translate this SBML document.

It prints the text to the stream given by the optional parameter stream. If no parameter is given, it prints the output to the standard error stream.

If no errors have occurred, i.e., getNumErrors() == 0, no output will be sent to the stream.

The format of the output is:

   N error(s):
     line NNN: (id) message
Parameters
streamthe ostream or ostringstream object indicating where the output should be printed.
Documentation note:
The native C++ implementation of this method defines a default argument value. In the documentation generated for different libSBML language bindings, you may or may not see corresponding arguments in the method declarations. For example, in Java and C#, a default argument is handled by declaring two separate methods, with one of them having the argument and the other one lacking the argument. However, the libSBML documentation will be identical for both methods. Consequently, if you are reading this and do not see an argument even though one is described, please look for descriptions of other variants of this method near where this one appears in the documentation.
See also
getNumErrors()
getErrorLog()
SBMLDocument.getError()
def libsbml.SBase.removeFromParentAndDelete (   self)
inherited

Python method signature(s):

removeFromParentAndDelete(SBase self)   int

Removes this object from its parent.

If the parent was storing this object as a pointer, it is deleted. If not, it is simply cleared (as in ListOf objects). This is a pure virtual method, as every SBase element has different parents, and therefore different methods of removing itself. Will fail (and not delete itself) if it has no parent object. This function is designed to be overridden, but for all objects whose parent is of the class ListOf, the default implementation will work.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.SBase.removeTopLevelAnnotationElement (   self,
  args 
)
inherited

Python method signature(s):

removeTopLevelAnnotationElement(SBase self, string elementName, string elementURI="", bool removeEmpty=True)   int
removeTopLevelAnnotationElement(SBase self, string elementName, string elementURI="")   int
removeTopLevelAnnotationElement(SBase self, string elementName)   int

Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and optional URI.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Calling this method allows a particular annotation element to be removed whilst the remaining annotations remain intact.

Parameters
elementNamea string representing the name of the top level annotation element that is to be removed
elementURIan optional string that is used to check both the name and URI of the top level element to be removed
removeEmptyif after removing of the element, the annotation is empty, and the removeEmpty argument is true, the annotation node will be deleted (default).
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
replaceTopLevelAnnotationElement()
replaceTopLevelAnnotationElement()
def libsbml.SBase.renameMetaIdRefs (   self,
  args 
)
inherited

Python method signature(s):

renameMetaIdRefs(SBase self, string oldid, string newid)

Renames all the meta-identifier attributes on this element.

In SBML, object 'meta' identifiers are of the XML data type ID; the SBML object attribute itself is typically named metaid. All attributes that hold values referring to values of type ID are of the XML data type IDREF. They are also sometimes informally referred to as 'metaid refs', in analogy to the SBML-defined type SIdRef.

This method works by looking at all meta-identifier attribute values, comparing the identifiers to the value of oldid. If any matches are found, the matching identifiers are replaced with newid. The method does not descend into child elements.

Parameters
oldidthe old identifier
newidthe new identifier
def libsbml.SBase.renameSIdRefs (   self,
  args 
)
inherited

Python method signature(s):

renameSIdRefs(SBase self, string oldid, string newid)

Renames all the SIdRef attributes on this element, including any found in MathML content (if such exists).

In SBML, object identifiers are of a data type called SId. In SBML Level 3, an explicit data type called SIdRef was introduced for attribute values that refer to SId values; in previous Levels of SBML, this data type did not exist and attributes were simply described to as 'referring to an identifier', but the effective data type was the same as SIdRefin Level 3. These and other methods of libSBML refer to the type SIdRef for all Levels of SBML, even if the corresponding SBML specification did not explicitly name the data type.

This method works by looking at all attributes and (if appropriate) mathematical formulas, comparing the identifiers to the value of oldid. If any matches are found, the matching identifiers are replaced with newid. The method does not descend into child elements.

Parameters
oldidthe old identifier
newidthe new identifier
def libsbml.SBase.renameUnitSIdRefs (   self,
  args 
)
inherited

Python method signature(s):

renameUnitSIdRefs(SBase self, string oldid, string newid)

Renames all the UnitSIdRef attributes on this element.

In SBML, unit definitions have identifiers of type UnitSId. In SBML Level 3, an explicit data type called UnitSIdRef was introduced for attribute values that refer to UnitSId values; in previous Levels of SBML, this data type did not exist and attributes were simply described to as 'referring to a unit identifier', but the effective data type was the same as UnitSIdRef in Level 3. These and other methods of libSBML refer to the type UnitSIdRef for all Levels of SBML, even if the corresponding SBML specification did not explicitly name the data type.

This method works by looking at all unit identifier attribute values (including, if appropriate, inside mathematical formulas), comparing the unit identifiers to the value of oldid. If any matches are found, the matching identifiers are replaced with newid. The method does not descend into child elements.

Parameters
oldidthe old identifier
newidthe new identifier
def libsbml.SBase.replaceTopLevelAnnotationElement (   self,
  args 
)
inherited

Python method signature(s):

replaceTopLevelAnnotationElement(SBase self, XMLNode annotation)   int
replaceTopLevelAnnotationElement(SBase self, string annotation)   int

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
replaceTopLevelAnnotationElement(XMLNode annotation)

Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

This method determines the name of the element to be replaced from the annotation argument. Functionally it is equivalent to calling removeTopLevelAnnotationElement(name) followed by calling appendAnnotation(annotation_with_name), with the exception that the placement of the annotation element remains the same.

Parameters
annotationXMLNode representing the replacement top level annotation
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
removeTopLevelAnnotationElement()
replaceTopLevelAnnotationElement()

Method variant with the following signature:
replaceTopLevelAnnotationElement(string annotation)

Replaces the given top-level element within the 'annotation' subelement of this SBML object and with the annotation element supplied.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

This method determines the name of the element to be replaced from the annotation argument. Functionally it is equivalent to calling removeTopLevelAnnotationElement(name) followed by calling appendAnnotation(annotation_with_name), with the exception that the placement of the annotation element remains the same.

Parameters
annotationstring representing the replacement top level annotation
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
removeTopLevelAnnotationElement()
replaceTopLevelAnnotationElement()
def libsbml.SBase.setAnnotation (   self,
  args 
)
inherited

Python method signature(s):

setAnnotation(SBase self, XMLNode annotation)   int
setAnnotation(SBase self, string annotation)   int

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
setAnnotation(XMLNode annotation)

Sets the value of the 'annotation' subelement of this SBML object.

The content of annotation is copied, and any previous content of this object's 'annotation' subelement is deleted.

Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Call this method will result in any existing content of the 'annotation' subelement to be discarded. Unless you have taken steps to first copy and reconstitute any existing annotations into the annotation that is about to be assigned, it is likely that performing such wholesale replacement is unfriendly towards other software applications whose annotations are discarded. An alternative may be to use SBase.appendAnnotation() or SBase.appendAnnotation().

Parameters
annotationan XML structure that is to be used as the new content of the 'annotation' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
getAnnotationString()
isSetAnnotation()
setAnnotation()
appendAnnotation()
appendAnnotation()
unsetAnnotation()

Method variant with the following signature:
setAnnotation(string annotation)

Sets the value of the 'annotation' subelement of this SBML object.

The content of annotation is copied, and any previous content of this object's 'annotation' subelement is deleted.

Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Call this method will result in any existing content of the 'annotation' subelement to be discarded. Unless you have taken steps to first copy and reconstitute any existing annotations into the annotation that is about to be assigned, it is likely that performing such wholesale replacement is unfriendly towards other software applications whose annotations are discarded. An alternative may be to use SBase.appendAnnotation() or SBase.appendAnnotation().

Parameters
annotationan XML string that is to be used as the content of the 'annotation' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
getAnnotationString()
isSetAnnotation()
setAnnotation()
appendAnnotation()
appendAnnotation()
unsetAnnotation()
def libsbml.SBMLDocument.setConsistencyChecks (   self,
  args 
)

Python method signature(s):

setConsistencyChecks(SBMLDocument self, long category, bool apply)

Controls the consistency checks that are performed when SBMLDocument.checkConsistency() is called.

This method works by adding or subtracting consistency checks from the set of all possible checks that SBMLDocument.checkConsistency() knows how to perform. This method may need to be called multiple times in order to achieve the desired combination of checks. The first argument (category) in a call to this method indicates the category of consistency/error checks that are to be turned on or off, and the second argument (apply, a boolean) indicates whether to turn it on (value of True) or off (value of False).

The possible categories (values to the argument category) are the set of constants whose names begin with the characters LIBSBML_CAT_ in the interface class libsbml. The following are the possible choices:

  • LIBSBML_CAT_GENERAL_CONSISTENCY: Correctness and consistency of specific SBML language constructs. Performing this set of checks is highly recommended. With respect to the SBML specification, these concern failures in applying the validation rules numbered 2xxxx in the Level 2 Versions 2–4 and Level 3 Version 1 specifications.

  • LIBSBML_CAT_IDENTIFIER_CONSISTENCY: Correctness and consistency of identifiers used for model entities. An example of inconsistency would be using a species identifier in a reaction rate formula without first having declared the species. With respect to the SBML specification, these concern failures in applying the validation rules numbered 103xx in the Level 2 Versions 2–4 and Level 3 Version 1 specifications.

  • LIBSBML_CAT_UNITS_CONSISTENCY: Consistency of measurement units associated with quantities in a model. With respect to the SBML specification, these concern failures in applying the validation rules numbered 105xx in the Level 2 Versions 2–4 and Level 3 Version 1 specifications.

  • LIBSBML_CAT_MATHML_CONSISTENCY: Syntax of MathML constructs. With respect to the SBML specification, these concern failures in applying the validation rules numbered 102xx in the Level 2 Versions 2–4 and Level 3 Version 1 specifications.

  • LIBSBML_CAT_SBO_CONSISTENCY: Consistency and validity of SBO identifiers (if any) used in the model. With respect to the SBML specification, these concern failures in applying the validation rules numbered 107xx in the Level 2 Versions 2–4 and Level 3 Version 1 specifications.

  • LIBSBML_CAT_OVERDETERMINED_MODEL: Static analysis of whether the system of equations implied by a model is mathematically overdetermined. With respect to the SBML specification, this is validation rule #10601 in the Level 2 Versions 2–4 and Level 3 Version 1 specifications.

  • LIBSBML_CAT_MODELING_PRACTICE: Additional checks for recommended good modeling practice. (These are tests performed by libSBML and do not have equivalent SBML validation rules.)

By default, all validation checks are applied to the model in an SBMLDocument object unless SBMLDocument.setConsistencyChecks() is called to indicate that only a subset should be applied. Further, this default (i.e., performing all checks) applies separately to each new SBMLDocument object created. In other words, each time a model is read using SBMLReader.readSBML(), SBMLReader.readSBMLFromString(), or the global functions readSBML() and readSBMLFromString(), a new SBMLDocument is created and for that document, a call to SBMLDocument.checkConsistency() will default to applying all possible checks. Calling programs must invoke SBMLDocument.setConsistencyChecks() for each such new model if they wish to change the consistency checks applied.

Parameters
categorya value drawn fromthe set of SBML error categories indicating the consistency checking/validation to be turned on or off.
applya boolean indicating whether the checks indicated by category should be applied or not.
See also
SBMLDocument.checkConsistency()
def libsbml.SBMLDocument.setConsistencyChecksForConversion (   self,
  args 
)

Python method signature(s):

setConsistencyChecksForConversion(SBMLDocument self, long category, bool apply)

Controls the consistency checks that are performed when SBMLDocument.setLevelAndVersion() is called.

This method works by adding or subtracting consistency checks from the set of all possible checks that may be performed to avoid conversion to or from an invalid document. This method may need to be called multiple times in order to achieve the desired combination of checks. The first argument (category) in a call to this method indicates the category of consistency/error checks that are to be turned on or off, and the second argument (apply, a boolean) indicates whether to turn it on (value of True) or off (value of False).

The possible categories (values to the argument category) are the set of constants whose names begin with the characters LIBSBML_CAT_ in the interface class libsbml. The following are the possible choices:

  • LIBSBML_CAT_GENERAL_CONSISTENCY: Correctness and consistency of specific SBML language constructs. Performing this set of checks is highly recommended. With respect to the SBML specification, these concern failures in applying the validation rules numbered 2xxxx in the Level 2 Versions 2–4 and Level 3 Version 1 specifications.

  • LIBSBML_CAT_IDENTIFIER_CONSISTENCY: Correctness and consistency of identifiers used for model entities. An example of inconsistency would be using a species identifier in a reaction rate formula without first having declared the species. With respect to the SBML specification, these concern failures in applying the validation rules numbered 103xx in the Level 2 Versions 2–4 and Level 3 Version 1 specifications.

  • LIBSBML_CAT_UNITS_CONSISTENCY: Consistency of measurement units associated with quantities in a model. With respect to the SBML specification, these concern failures in applying the validation rules numbered 105xx in the Level 2 Versions 2–4 and Level 3 Version 1 specifications.

  • LIBSBML_CAT_MATHML_CONSISTENCY: Syntax of MathML constructs. With respect to the SBML specification, these concern failures in applying the validation rules numbered 102xx in the Level 2 Versions 2–4 and Level 3 Version 1 specifications.

  • LIBSBML_CAT_SBO_CONSISTENCY: Consistency and validity of SBO identifiers (if any) used in the model. With respect to the SBML specification, these concern failures in applying the validation rules numbered 107xx in the Level 2 Versions 2–4 and Level 3 Version 1 specifications.

  • LIBSBML_CAT_OVERDETERMINED_MODEL: Static analysis of whether the system of equations implied by a model is mathematically overdetermined. With respect to the SBML specification, this is validation rule #10601 in the Level 2 Versions 2–4 and Level 3 Version 1 specifications.

  • LIBSBML_CAT_MODELING_PRACTICE: Additional checks for recommended good modeling practice. (These are tests performed by libSBML and do not have equivalent SBML validation rules.)

By default, all validation checks are applied to the model in an SBMLDocument object unless SBMLDocument.setConsistencyChecks() is called to indicate that only a subset should be applied. Further, this default (i.e., performing all checks) applies separately to each new SBMLDocument object created. In other words, each time a model is read using SBMLReader.readSBML(), SBMLReader.readSBMLFromString(), or the global functions readSBML() and readSBMLFromString(), a new SBMLDocument is created and for that document, a call to SBMLDocument.checkConsistency() will default to applying all possible checks. Calling programs must invoke SBMLDocument.setConsistencyChecks() for each such new model if they wish to change the consistency checks applied.

Parameters
categorya value drawn fromthe set of SBML error categories indicating the consistency checking/validation to be turned on or off.
applya boolean indicating whether the checks indicated by category should be applied or not.
See also
SBMLDocument.setLevelAndVersion()
def libsbml.SBMLDocument.setLevelAndVersion (   self,
  args 
)

Python method signature(s):

setLevelAndVersion(SBMLDocument self, long level, long version, bool strict=True, bool ignorePackages=False)   bool
setLevelAndVersion(SBMLDocument self, long level, long version, bool strict=True)   bool
setLevelAndVersion(SBMLDocument self, long level, long version)   bool

Sets the SBML Level and Version of this SBMLDocument instance, attempting to convert the model as needed.

This method is the principal way in libSBML to convert models between Levels and Versions of SBML. Generally, models can be converted upward without difficulty (e.g., from SBML Level 1 to Level 2, or from an earlier Version of Level 2 to the latest Version of Level 2). Sometimes models can be translated downward as well, if they do not use constructs specific to more advanced Levels of SBML.

Before calling this method, callers may check compatibility directly using the methods SBMLDocument.checkL1Compatibility(), SBMLDocument.checkL2v1Compatibility(), SBMLDocument.checkL2v2Compatibility(), SBMLDocument.checkL2v3Compatibility(), SBMLDocument.checkL2v4Compatibility(), and SBMLDocument.checkL3v1Compatibility().

The valid combinations of SBML Level and Version as of this release of libSBML are the following:

  • Level 1 Version 2
  • Level 2 Version 1
  • Level 2 Version 2
  • Level 2 Version 3
  • Level 2 Version 4
  • Level 3 Version 1

Strict conversion applies the additional criteria that both the source and the target model must be consistent SBML. Users can control the consistency checks that are applied using the SBMLDocument.setConsistencyChecksForConversion() method. If either the source or the potential target model have validation errors, the conversion is not performed. When a strict conversion is successful, the underlying SBML object model is altered to reflect the new level and version. Thus, information that cannot be converted (e.g. sboTerms) will be lost.

Parameters
levelthe desired SBML Level
versionthe desired Version within the SBML Level
strictboolean indicating whether to check consistency of both the source and target model when performing conversion (defaults to true )
ignorePackagesboolean indicating whether the presence of packages should be ignored by the conversion routine (defaults to false )
Returns
True if the level and version of the document were successfully set to the requested values (which may have required conversion of the model), False otherwise.
Note
Calling this method will not necessarily lead to a successful conversion. If the conversion fails, it will be logged in the error list associated with this SBMLDocument. Callers should consult getNumErrors() to find out if the conversion succeeded without problems. For conversions from Level 2 to Level 1, callers can also check the Level of the model after calling this method to find out whether it is Level 1. (If the conversion to Level 1 failed, the Level of this model will be left unchanged.)
Documentation note:
The native C++ implementation of this method defines a default argument value. In the documentation generated for different libSBML language bindings, you may or may not see corresponding arguments in the method declarations. For example, in Java and C#, a default argument is handled by declaring two separate methods, with one of them having the argument and the other one lacking the argument. However, the libSBML documentation will be identical for both methods. Consequently, if you are reading this and do not see an argument even though one is described, please look for descriptions of other variants of this method near where this one appears in the documentation.
See also
checkL1Compatibility()
checkL2v1Compatibility()
checkL2v2Compatibility()
checkL2v3Compatibility()
checkL2v4Compatibility()
checkL3v1Compatibility()
checkL3v1Compatibility()
def libsbml.SBMLDocument.setLocationURI (   self,
  args 
)

Python method signature(s):

setLocationURI(SBMLDocument self, string uri)

Sets the location of this SBMLDocument.

Called automatically when readSBMLFromFile is used, but may be set manually as well.

def libsbml.SBase.setMetaId (   self,
  args 
)
inherited

Python method signature(s):

setMetaId(SBase self, string metaid)   int

Sets the value of the meta-identifier attribute of this object.

The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use the XML ID type. Although SBML itself specifies the use of XML ID only for the 'metaid' attribute, SBML-compatible applications should be careful if they use XML ID's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.

The string metaid is copied.

Parameters
metaidthe identifier string to use as the value of the 'metaid' attribute
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
getMetaId()
isSetMetaId()
def libsbml.SBMLDocument.setModel (   self,
  args 
)

Python method signature(s):

setModel(SBMLDocument self, Model m)   int

Sets the Model for this SBMLDocument to a copy of the given Model.

Parameters
mthe new Model to use.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
createModel()
getModel()
def libsbml.SBase.setModelHistory (   self,
  args 
)
inherited

Python method signature(s):

setModelHistory(SBase self, ModelHistory history)   int

Sets the ModelHistory of this object.

The content of history is copied, and this object's existing model history content is deleted.

Parameters
historyModelHistory of this object.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.
def libsbml.SBase.setNamespaces (   self,
  args 
)
inherited

Python method signature(s):

setNamespaces(SBase self, XMLNamespaces xmlns)   int

Sets the namespaces relevant of this SBML object.

The content of xmlns is copied, and this object's existing namespace content is deleted.

The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core.

Parameters
xmlnsthe namespaces to set
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.SBase.setNotes (   self,
  args 
)
inherited

Python method signature(s):

setNotes(SBase self, XMLNode notes)   int
setNotes(SBase self, string notes, bool addXHTMLMarkup=False)   int
setNotes(SBase self, string notes)   int

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
setNotes(string notes, bool addXHTMLMarkup = false)

Sets the value of the 'notes' subelement of this SBML object to a copy of the string notes.

The content of notes is copied, and any existing content of this object's 'notes' subelement is deleted.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

The following code illustrates a very simple way of setting the notes using this method. Here, the object being annotated is the whole SBML document, but that is for illustration purposes only; you could of course use this same approach to annotate any other SBML component.

Parameters
notesan XML string that is to be used as the content of the 'notes' subelement of this object
addXHTMLMarkupa boolean indicating whether to wrap the contents of the notes argument with XHTML paragraph (<p>) tags. This is appropriate when the string in notes does not already containg the appropriate XHTML markup.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
getNotesString()
isSetNotes()
setNotes()
appendNotes()
appendNotes()
unsetNotes()
SyntaxChecker.hasExpectedXHTMLSyntax()

Method variant with the following signature:
setNotes(XMLNode notes)

Sets the value of the 'notes' subelement of this SBML object.

The content of notes is copied, and any existing content of this object's 'notes' subelement is deleted.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

Parameters
notesan XML structure that is to be used as the content of the 'notes' subelement of this object
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
getNotesString()
isSetNotes()
setNotes()
appendNotes()
appendNotes()
unsetNotes()
SyntaxChecker.hasExpectedXHTMLSyntax()
def libsbml.SBMLDocument.setPackageRequired (   self,
  args 
)

Python method signature(s):

setPackageRequired(SBMLDocument self, string package, bool flag)   int

Sets the required attribute value of the given package extension.

Note
The name of package must not be given if the package is not enabled.
Parameters
packagethe name or URI of the package extension.
flagBoolean value indicating whether the package is required.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.SBMLDocument.setPkgRequired (   self,
  args 
)

Python method signature(s):

setPkgRequired(SBMLDocument self, string package, bool flag)   int

Sets the value of the required attribute for the given package.

Note
The name of package must not be given if the package is not enabled.
Parameters
packagethe name or URI of the package extension.
flaga Boolean value.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.SBase.setSBOTerm (   self,
  args 
)
inherited

Python method signature(s):

setSBOTerm(SBase self, int value)   int
setSBOTerm(SBase self, string sboid)   int

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
setSBOTerm(int value)

Sets the value of the 'sboTerm' attribute.

Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers.

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.

Parameters
valuethe NNNNNNN integer portion of the SBO identifier
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
setSBOTerm()

Method variant with the following signature:
setSBOTerm(string &sboid)

Sets the value of the 'sboTerm' attribute by string.

Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers. This method lets you set the value of 'sboTerm' as a complete string of the form 'SBO:NNNNNNN', whereas setSBOTerm(int value) allows you to set it using the integer form.

SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.

Parameters
sboidthe SBO identifier string of the form 'SBO:NNNNNNN'
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
setSBOTerm()
def libsbml.SBase.toSBML (   self)
inherited

Python method signature(s):

toSBML(SBase self)   string *

Returns a string consisting of a partial SBML corresponding to just this object.

Returns
the partial SBML that describes this SBML object.
Warning
This is primarily provided for testing and debugging purposes. It may be removed in a future version of libSBML.
def libsbml.SBase.toXMLNode (   self)
inherited

Python method signature(s):

toXMLNode(SBase self)   XMLNode

Returns this element as an XMLNode.

Returns
this element as an XMLNode.
Warning
This operation is computationally expensive, because the element has to be fully serialized to a string and then parsed into the XMLNode structure. Attempting to convert a large tree structure (e.g., a large Model) may consume significant computer memory and time.
def libsbml.SBase.unsetAnnotation (   self)
inherited

Python method signature(s):

unsetAnnotation(SBase self)   int

Unsets the value of the 'annotation' subelement of this SBML object.

Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content.

SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
getAnnotation()
getAnnotationString()
isSetAnnotation()
setAnnotation()
setAnnotation()
appendAnnotation()
appendAnnotation()
def libsbml.SBase.unsetCVTerms (   self)
inherited

Python method signature(s):

unsetCVTerms(SBase self)   int

Clears the list of CVTerm objects attached to this SBML object.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.SBase.unsetId (   self)
inherited

Python method signature(s):

unsetId(SBase self)   int

Unsets the value of the 'id' attribute of this SBML object.

Most (but not all) objects in SBML include two common attributes: 'id' and 'name'. The identifier given by an object's 'id' attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.SBase.unsetMetaId (   self)
inherited

Python method signature(s):

unsetMetaId(SBase self)   int

Unsets the value of the 'metaid' attribute of this SBML object.

The optional attribute named 'metaid', present on every major SBML component type, is for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. The latter point is important, because the uniqueness criterion applies across any attribute with type ID anywhere in the file, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use the XML ID type. Although SBML itself specifies the use of XML ID only for the 'metaid' attribute, SBML-compatible applications should be careful if they use XML ID's in XML portions of a model that are not defined by SBML, such as in the application-specific content of the 'annotation' subelement. Finally, note that LibSBML does not provide an explicit XML ID data type; it uses ordinary character strings, which is easier for applications to support.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.SBase.unsetModelHistory (   self)
inherited

Python method signature(s):

unsetModelHistory(SBase self)   int

Unsets the ModelHistory object attached to this object.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
Note
In SBML Level 2, model history annotations were only permitted on the Model element. In SBML Level 3, they are permitted on all SBML components derived from SBase.
def libsbml.SBase.unsetName (   self)
inherited

Python method signature(s):

unsetName(SBase self)   int

Unsets the value of the 'name' attribute of this SBML object.

Most (but not all) objects in SBML include two common attributes: 'id' and 'name'. In contrast to the 'id' attribute, the 'name' attribute is optional and is not intended to be used for cross-referencing purposes within a model. Its purpose instead is to provide a human-readable label for the component. The data type of 'name' is the type string defined in XML Schema. SBML imposes no restrictions as to the content of 'name' attributes beyond those restrictions defined by the string type in XML Schema.

The recommended practice for handling 'name' is as follows. If a software tool has the capability for displaying the content of 'name' attributes, it should display this content to the user as a component's label instead of the component's 'id'. If the user interface does not have this capability (e.g., because it cannot display or use special characters in symbol names), or if the 'name' attribute is missing on a given component, then the user interface should display the value of the 'id' attribute instead. (Script language interpreters are especially likely to display 'id' instead of 'name'.)

As a consequence of the above, authors of systems that automatically generate the values of 'id' attributes should be aware some systems may display the 'id''s to the user. Authors therefore may wish to take some care to have their software create 'id' values that are: (a) reasonably easy for humans to type and read; and (b) likely to be meaningful, for example by making the 'id' attribute be an abbreviated form of the name attribute value.

An additional point worth mentioning is although there are restrictions on the uniqueness of 'id' values, there are no restrictions on the uniqueness of 'name' values in a model. This allows software applications leeway in assigning component identifiers.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.SBase.unsetNotes (   self)
inherited

Python method signature(s):

unsetNotes(SBase self)   int

Unsets the value of the 'notes' subelement of this SBML object.

The optional SBML element named 'notes', present on every major SBML component type, is intended as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. Every object derived directly or indirectly from type SBase can have a separate value for 'notes', allowing users considerable freedom when adding comments to their models.

The format of 'notes' elements must be XHTML 1.0. To help verify the formatting of 'notes' content, libSBML provides the static utility method SyntaxChecker.hasExpectedXHTMLSyntax(); however, readers are urged to consult the appropriate SBML specification document for the Level and Version of their model for more in-depth explanations. The SBML Level 2 and  3 specifications have considerable detail about how 'notes' element content must be structured.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
getNotesString()
isSetNotes()
setNotes()
setNotes()
appendNotes()
appendNotes()
SyntaxChecker.hasExpectedXHTMLSyntax()
def libsbml.SBase.unsetSBOTerm (   self)
inherited

Python method signature(s):

unsetSBOTerm(SBase self)   int

Unsets the value of the 'sboTerm' attribute of this SBML object.

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.SBMLDocument.validateSBML (   self)

Python method signature(s):

validateSBML(SBMLDocument self)   long

Performs consistency checking and validation on this SBML document.

If this method returns a nonzero value (meaning, one or more consistency checks have failed for SBML document), the failures may be due to warnings or errors. Callers should inspect the severity flag in the individual SBMLError objects returned by SBMLDocument.getError() to determine the nature of the failures.

Note
unlike checkConsistency this method will write the document in order to determine all errors for the document. This will also clear the error log.
Returns
the number of failed checks (errors) encountered.
See also
SBMLDocument.checkConsistency()